Dan,
There are four PHP config directives which can be used in Apache's httpd.conf. They are:
php_value
php_flag
php_admin_value
php_admin_flag
More info on these guys can be found at: http://www.php.net/manual/en/configuration.php.
To use your example of differing max_execution_time, in the vhost directive for vhost A you would do:
php_value max_execution_time 30
and in the directive for vhost B:
php_value max_execution_time 60
HTH.
geoff